Part 1

This second mission begins fairly seamlessly with where the lengthy introductory mission concludes. Sally will have brought you to a cryogenics facility on the ship where four humans have been frozen in stasis for god-knows-how-long. By pressing a switch in front of you, in the middle of the four cryogenic chambers (two on each side), you can release them from their long static existence. By doing so, you'll now have four humans from various points in the Earth's (relatively) recent past to help you on future endeavors during this second mission. So while you don't necessarily have to free them, you ought to anyway. After all four are freed, speak to each of them to learn a little bit about them.

Paulson is a cowboy, probably from 19th century America. When you claim you're on a ship, he claims you're lying, because the ship isn't rocking back and forth, and there's no sound of water. Oy vey. Private Tercorien was a US Army medic during the war back in 2077 that eventually led to a nuclear exchange, and therefore, quintessential MAD. He's confused and scared, but actually quite useful, since he can turn all of those Alien Biogels you've been finding into useable Adapted Biogel, which exponentially raises its effectiveness. And then, there's Toshiro Kago, a samurai who speaks no English. Taken from Earth perhaps a thousand years ago, there's no communicating with this man. The fourth person cryogenically frozen, an astronaut, falls limp to the ground. Unfortunately, he's dead. But that works to your advantage, as you'll soon learn.

Alien Logs

Please note that if you want to acquire all twenty-five Alien Logs, you're going to have to deviate from our walkthrough to visit two completely optional sections of the Mothership Zeta. Both can only be accessed from the Engineering Core, and once you leave that area (more specifically, once you undertake the spacewalk segment at the end of this mission), you won't be able to return.

The first optional area is the Maintenance Level, which can be accessed via an active teleportation device just off of the center of the core. This area will involve you getting into a broken garbage elevator with Sally as she fixes it and brings you from floor to floor. Eventually, you'll be able to get out of the elevator and walk around the Waste Disposal area thereafter. Near the end of this area, right before Sally gives you a way to reach the core once more, you'll be able to grab Alien Log #19.

The other two Alien Logs are found via the Cargo Hold, which is a door also off the center of the Engineering Core. Traverse the Cargo Hold until you reach an area marked as Research Lab off of it. This area contains both Alien Logs you seek. In the initial room, you'll find Alien Log #13, and in the subsequent room, you can find Alien Log #21. When these three stray Alien Logs are combined with the twenty-two we find for you in the walkthrough itself, that makes twenty-five. That's all of them!

Off of the body of the dead astronaut, you'll find a Spacesuit. A spacewalk will soon be necessary to continue, and that Spacesuit will allow you to survive the extremes of cold, dead space. Grab it, but don't yet equip it. There's work to be done. Those locked doors we told you to ignore during the last mission, which led to places like the hangar and robot assembly area, are now going to be our destination targets. Because Sally knows how to unlock those doors (and does just that for you), you're now free to explore them in any order you so desire. We're going to start, in this walkthrough, with the Cryo Lab.

Once within the Cryo Lab, you'll be surrounded by the endless smoke and blue hue of the various freezing mechanisms around you. A lone enemy will greet you here, an alien wielding a powerful pistol. Quickly dispatch him, and then take a breather, because there are no other enemies of any consequence anywhere else in your vicinity. Move forward and seek out a switch marked as a Release Mechanism. Hit it, and then seek out a pathway leading rightward towards a down-sloping staircase. Ignore the stairs for the time being, and pillage the goods out of the nearby container instead. Nestled next to a non-functioning teleporter, you'll find all sorts of standard alien gear in there, including an Alien Disintegrator and some Alien Power Modules.

Part 2

After grabbing those goods, head down the staircase and continue to explore. The large table tucked underneath the staircase contains both Large Alien Crystals and Small Alien Crystals, so be sure to grab both of those. It's the room to the right of the staircase (if you're facing it) that's of real interest, however, and it appears that the switch you hit above will grant you access to this room. Not only is a healing device in this room for your use, but there are three containers and some tables littered with goods as well. You'll find more of the standard alien fare you should be used to finding at this point, but on the tables and in the containers, you'll also find things far more strange -- objects from Earth. A thorough investigation will lead you to finding, amongst other goods, 10mm Rounds, 5.56mm Rounds, Abraxo Cleaner, Rad-X, Vodka, and even a Pressure Cooker. Most importantly is Alien Log #4, however, which can be acquired by examining the circular device down here, along one of the large computer consoles.

When you've stocked up on goods, head back to the top floor and continue forward from the entrance to explore an entirely new area. The right and left sides of this room seem like mirror images of one another. There's a room off of the square-shaped corridor to your right, and to your left. There are two downed robots, one to your right, and one to your left. There are two bins full of alien items, one on your right, and one on your left. Well, you get the idea. The first thing you're going to want to do is reprogram each robot, first by realigning their sensors, and then turning them on. Then, go ahead and pillage the goods from the two containers, one on each side of the pathway. You'll find more of the same -- Alien Epoxy, Alien Disintegrators, Alien Atomizers, Small Alien Crystals, Large Alien Crystals, and on and on. Add what you need to your inventory, and leave the rest behind.

With the droids reprogrammed and the goods acquired, you can now use the switches alongside the glass looking into either room to activate the cryogenically-based machines occupying the majority of both rooms. Since you've reprogrammed the robots, one will go into each room and help you fight off the Ghoul-type enemies that appear in each room (Raider encounters are also possible), two per room out of two machines. Glowing Ones might be among the Ghouls let loose, but for the most part, even if the foes are hard, they are far easier to deal with than the aliens you've been fighting in your short time on the mothership. Repeat the process in both rooms, killing any aliens that might be present as well. Then, when both machines have been activated and their contents destroyed, you can move through the next blast door into the subsequent corridor. If you're collecting alien logs, be sure to acquire Alien Log #2 before continuing onward. It's located in one of the rooms off of the main path.

The linear corridor from the previous room will eventually lead to a control room on your left, and a gigantic experimentation and storage area straight ahead. For the time being, you should bear leftward into the control room, where you can find some goods on a table, including Alien Worm Food. You'll also find a control unit, but for the time being, ignore it. Instead, work your way into the adjoining room, which is quite vast. Here, you'll find some enemy resistance. Kill the aliens roving around the various corridors working their way in a labyrinthine fashion in and out of various machines. Also, destroy the gun turret smartly-placed in one corner. Then, when all is quiet, work your way back to the adjacent control room.

Now that the aliens have been quieted in the next room, you can use the control panel. This will cause more cryogenic freezing chambers to rise up and let go of their captives. While you could have let the aliens and the captives fight it out, it's worth more experience to you to kill as many enemies as possible, which is why we sent you in ahead of time to kill the alien contingent before letting their prisoners loose. The prisoners that are let loose are primarily Ghoul-related, but can also marked as Raiders. Both are enemies on the Earth's surface, and here, things are no different. Be especially careful of the Raiders, since they'll loot dead alien bodies for weapons and quickly turn them on you. Kill all released enemies, and scour their bodies for anything you might want before proceeding onward. Also, if you want more Earth-based goods of a random variety, you can find them in the downstairs portion of this cryogenics locale. Mentats, Stimpaks, Med-X and Psycho are probably going to be the most valuable stuff you'll find down there, but there's plenty of other crap to pick through if you want to take the time to do it.

Part 3

When you're done here, continue out of this large area via the only unexplored conduit you've yet to go down. This winding pathway will ultimately lead to an empty room with a control panel and two locked doors. Through the glass, you'll see some aliens doing all sorts of experiments on captured humans. However, when you try to go through either locked door, you'll be stopped. There's simply no way through. The nearby control panel is the key. Activate it, and the cryogenic machines will suddenly kick in. Once they do, the humans will be killed, but so too will the aliens doing experiments on them. Furthermore, the doors will open, allowing to access to the room. Before you push on through, be sure to grab any human goods you want from both sides of the room. An Advanced Radiation Suit, Rad-X and Purified Water are among the more valuable plunder.

At the top end of this room, you'll find two more familiar devices. These devices, the circular objects with three blue lights in the middle of each of them, contain two more audio logs. Activate both to grab Alien Log #11 and Alien Log #17. Then, press into the next room. It appears that, for whatever reason, the switch in here doesn't work. The aliens may have used it before they died, or it may be broken. Either way, it means that there's little else to do here. Press forward through the next door, and into a new location called Cryo Storage.

In this new area, you won't immediately run into any enemies. The first thing you're going to want to do is run to your left and examine the circular computer terminal there, where Alien Log #25 can be acquired. Now, the room splits off to the right and to the left, and you can take either corridor to your next destination. But first, examine the two containers on either side of the room, where virtually-identical caches of items can be found in both. All of the usual suspects are in each, Alien Crystals, Alien Epoxy and the like. Then, head out of the room via either the right or the left pathway, and have your firearm-of-choice at the ready, because you'll begin to encounter a slew of enemies as you work your way into the next room.

This next room is the last large room where you'll find an enemy contingent in the cryogenics area of the ship. And enemies are found here in vast quantities. Since you're in the storage area of the Mothership Zeta, expect to find more types of enemies than just the standard alien types you've been fighting thusfar. Indeed, you'll fight enemies as simple as Ghouls and as difficult as Super Mutant Masters. It all depends on how long you let the alien controllers live, because they (or you, if you want) can access various control terminals to let these enemies loose. A little trick to employ if you find yourself overwhelmed is to draw your enemies towards a chamber that hasn't yet been activated. When they get close, use the nearby switch to activate it, and you should freeze the aliens into a stasis-laden death. Otherwise, there's nothing too interesting here. You can explore the smoky underbelly of this location, but the only important thing you'll find down there is Alien Log #16, which you should be sure to grab before proceeding.

When you're done in that large room, press forward into the final area of the cryogenics facility. You can do this via a number of conduits, but all of the hallways lead ultimately to an identical area. Here, the much sought-after generator can be found. Remember destroying the cryogenics generator in the engineering core? You'll use an identical series of commands here for equally-identical results. Turn the generator on via the power switch. Then, when the three coolant devices show up, activate each of them. Then, watch the generator go boom. And even though you've found a great many teleporter strewn around the ship that are inactive, the one in the room with you can be activated via a switch. Use it to get to an earlier location in the cryogenics lab, and then ultimately, head back to the engineering core and meet up with your fellow human survivors.

Part 4

Next up is the robot assembly area. If your back is facing the cryogenics lab, go back towards the center of the engineering core, and veer leftward. You'll find the door leading to this area there. As soon as you enter, you won't run into any enemies immediately. Move forward and grab the Large Alien Crystals from the top of the box on your right, and as you move forward some more, you'll find Alien Worm Food sitting on a table. Otherwise, there are a couple of containers strewn about that hold your typical alien fare; the same stuff you've been finding over and over again as you move through the mothership. When you press forward far enough that you run into a staircase leading downward, go ahead and take it.

Once down the stairs, the path will bring you in a linear direction forward, and then swing rightward, where it will again lead forward. All rooms off of this path, which will be on your left going forward, are filled with broken teleportation devices, and little else, so they can be ignored entirely. However, you will run into plenty of robotic enemies down here (they spawn from those very teleportation devices), so have your firearm at the ready. In addition to the normal security drones you've run into so far, you'll also be dealing with Guardian Drones, which can attack from afar with great precision and power. Thankfully, they are relatively weak defensively, so even though you'll be dealing with quite a number of them moving forward, you should have little difficulty in taking them out. As you move forward, keep an eye out for any items you may want to grab off of crates and shelves, and also loot the lone container at the far end of the corridor. You should be able to walk away with, amongst other goods, plenty of Large Alien Crystals, Small Alien Crystals, and Alien Epoxy.

From the location of the container, head through the door and work your way into yet another area of the robot assembly station. The glass-contained conveyor belt we saw earlier continues to run through this room, and you'll find more robotic resistance here in addition to a few aliens packing their usual powerful firearms. Feel free to explore if you want to grab more Small Alien Crystals and Large Alien Crystals (the abundance of these devices here could indicate that they're the power source for the aliens' robotic companions), but there's not much else to find here. There are two things of importance that you'll need to explore, however. As you move forward through the room, parallel to the conveyor belt, you'll see a switch on your left. Hit this switch -- it activates a nearby teleporter that you'll use in a little while. Then, continue forward until you reach a control panel on an enclosed part of the conveyor belt. Examine it and set it to detonate. This will blow a hole in the side of the conveyor belt that you can then crawl through to continue.

At this point, we're nearing the end of the robot assembly area, so resistance will be at its absolute staunchest here. Not only have you destroyed the assembly line for the alien robots, but you've been otherwise running around the Mothership Zeta willy-nilly up to this point, so it should come as no surprise that the aliens are pretty pissed off. You'll be fighting both aliens and Guardian Drones here. Your best bet, believe it or not, is to try and lure your enemies towards you, as opposed to fighting them out in the open. Run out in the room via the conveyor belt, and when enemies spot you, run back into the tunnel you just blew a hole through. They'll be forced to file together in order to strike you, which makes them easy targets. Be sure to prioritize destroying Guardian Drones before aliens, though, as they pack a much, much more powerful punch.

Once you've successfully nullified the immediate threat here, you can then begin to explore the room. Head rightward and expect for more aliens to be drawn out from the location above (all Guardian Drones should have been brought out by this point). Aliens can draw out more robots if you let them live long enough to visit the various holding cells for droids just off the production line, so fell them as quickly as you can. As usual, everything from Small Alien Crystals to Alien Epoxy can be found if you explore both the upstairs portion of this room and the various tunnels that run underneath it and around it. You can also find typical alien items in a few containers as well. But it's what's down the stairs adjacent to the raised area of the room that's of most concern.

Part 5

Why is this? Well, it's because down those stairs, you'll find what it is you've been looking for all this time -- the generator that powers the robot assembly plant. If you're following this walkthrough, you've now destroyed two of these generators (and even if you're not following this walkthrough to a tee, you must have destroyed at least one), so you should know how to do this by now. Turn on the machine, activate the cooling devices, and watch it all explode gloriously. Once this happens, you can head down the semi-hidden pathway underneath the stairs. This leads to -- you guessed it -- a teleportation device, which will bring you closer to the entrance/exit of the assembly area. Since you've likely felled all enemies up to this point, you should be able to run back to the entrance and reach the engineering core without being assaulted even once.

Once you've returned to the engineering core, you should be greeted by Sally, who will congratulate you on a job well done thus far (if there's only one generator left, that is). And for us, that last generator is located in the hangar bay of the Mothership Zeta, located clear across the engineering core from the entrance to the robot assembly plant. As soon as you're inside, loot the container directly in front of you for normal alien items, and then follow the linear corridor, which will lead (after descending a staircase) to the hangar itself. This small area off of the hangar, which is to your right, contains another container to pillage. You can also grab items, like Small Alien Crystals, from the shelves lining the right wall. But to proceed with the mission at hand, head leftward.

Walk down the stairs and approach the location of the lone alien craft, seemingly hanging in midair. Work your way around it on either side. The doors on your left will be sealed shut for now, but we'll be able to take care of that shortly. On the other end of the ship is another staircase leading upward. There are a few alien enemies guarding this platform, including some of those pesky stealth aliens we found earlier. We'll be fighting them en masse soon enough, but for now, take out the limited number of alien adversaries you meet on the far side of the ship. The nearby switch they were guarding is key. Once you hit it, many of the force fields that were surrounding doors in your vicinity will be downed, allowing you to proceed. This includes not only the door near the entrance to the hangar that was sealed off, but the door nearby, and even a few of the doors we passed as we walked around the spaceship.

If you want to be thorough for later, go ahead and backtrack towards the doors near the space fighter hanging midair. Not all of the doors will be unsealed there yet (and you'll find out why soon enough), but in the meantime, clear the corridors of the gun turrets you find. Then, you can use either unsealed door on the right or left end of the hangar to proceed -- so, either the one near the switch that unsealed the doors, or the one closer to the entrance to the hangar will do. They both lead to identical rooms. Again, this room is completely empty, but it's what happens when you hit the lone switch along another sealed door that's of real importance. Get ready for one hell of a fight. (If you're curious about the five switches that control the suspended ship in the hangar, it's unclear what they do, so you can ignore them completely.)

When you hit the switch near the sealed door, you may be excited. After all, the generator is clearly on the other side of the seal. But an alarm will sound when the switch is struck, releasing all sorts of enemies into the hangar proper. Only after you deal with the enemy force in its entirety will you be able to proceed with the final segment of the mission -- more specifically, the destruction of the final generator. So, get your guns ready, make sure you best armor is equipped... you may even want to take a Buffout or some other drugs to be sure you're ready. Because this upcoming battle is quite the battle, indeed.

Part 6

To survive this encounter without ripping through your store of healing items, getting your armor destroyed, and using more ammunition than is necessary, you're going to have to be smart. Your best bet is to keep the high ground near the staircase that leads down towards the hangar. That way, alien enemies can come up and greet you, and you can initiate assaults on them. If you're extra savvy, you can even line the stairs with mines that will chip away at their damage, making them easier to take when they get up to you. Regular aliens will be mixed in with the extra-pesky cloaked enemies, in addition to quite a few Guardian Drones that will appear. For the latter, you're going to have to fire down on them, because there's no way they can climb the stairs to greet you. And unfortunately, those are the foes that can deal the most damage to you. So, keep a careful eye on your health.

Okay, so are all of the enemies defeated? All of them? When they've all been felled, which will take some time, feel free to explore the rooms on the left side of the hangar that the enemies were pouring in from (via multiple teleportation devices, if you're curious). You can find plenty of items in a few containers there, and even more of the standard alien items on shelves and on top of crates. Then, backtrack to where you initially hit the switch that summoned all of these enemies. The barrier blocking the nearby door will have disappeared, granting you access to the hangar's generator. You should know what to do by now -- obliterate that damn generator, once and for all.

If you've been following our walkthrough up to this point, then the hangar's generator will be the fourth and final one you had to destroy. That means that all that's left to do is visit with Sally back in the engineering core. When you return to the core, expect to find your new friends doing battle with a few aliens that have shown up on the scene. Help them out if you want, but your main priority here should be to find Sally and speak with her. She'll be brief with you, telling you that all that's left to do is to finally undertake your epic spacewalk via the door on the far end of the wing. The door will be marked as the airlock door to the decompression chamber. Head on through, and shortly thereafter, you'll have to get ready for a bona fide spacewalk in zero G.

As soon as you get through the door, play it safe and equip your Spacesuit, since having it on is the only hope you have of surviving once you reach the zero G environment surrounding the ship. But first, you'll need to traverse a pretty linear series of corridors and staircases towards the door leading out into space. If you want to be really thorough, you can explore the little nooks and crannies of the path to find containers and item-lined shelves. But to be frank, you are probably drowning in Alien Epoxy and Crystals at this point, no? Well, nonetheless, explore at will, but what you're really seeking out is the door leading outside. Literally.

When you're outside, take a look at your surroundings. You're stuck to the ship, but you're out in space. At the center of the area is a teleportation device that leads up to the top tier of the ship, but for now, it's disabled. What to do!? Well, it's easy. You'll find three raised panels on the surface of the ship. When you reach each one of them, examine them and you'll be able to send them back down into position. These three panels are rather easy to find if you just walk around in a circle, though they are at varying distances from the teleportation device, so be sure to spread out a little bit. After the third panel is pushed down and reactivated, the teleportation device will begin functioning. All that's left to do is take it up to the top tier of the ship, where Mothership Zeta's final mission will begin in earnest.